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B C D E F G I L M N P R S T U W misc
| genoset-package | GenoSet: An eSet for data with genome locations |
| baf | Get baf data |
| baf-method | Get baf data |
| baf2mbaf | Calculate mBAF from BAF |
| baf<- | Get baf data |
| baf<--method | Get baf data |
| BAFSet | Create a BAFSet object |
| BAFSet-class | Class '"BAFSet"' |
| BAFSet-defunct | Create a BAFSet object |
| BAFSet.to.ExpressionSets | Make a pair of ExpressionSets from a BAFSet |
| BAFSet.to.ExpressionSets-defunct | Make a pair of ExpressionSets from a BAFSet |
| boundingIndices | Find indices of features bounding a set of chromosome ranges/genes |
| boundingIndices2 | Find indices of features bounding a set of chromosome ranges/genes |
| boundingIndicesByChr | Find indices of features bounding a set of chromosome ranges/genes, across chromosomes |
| bounds2Rle | Convert bounding indices into a Rle |
| calcGC | Calculate GC Percentage in windows |
| chr | Look up chromosome for each feature |
| chr-method | Look up chromosome for each feature |
| chrIndices | Get a matrix of first and last index of features in each chromosome |
| chrIndices-method | Get a matrix of first and last index of features in each chromosome |
| chrInfo | Chromosome Information |
| chrInfo-method | Chromosome Information |
| chrNames | Get list of unique chromosome names |
| chrNames-method | Get list of unique chromosome names |
| chrNames<- | Get list of unique chromosome names |
| chrNames<--method | Get list of unique chromosome names |
| chrOrder | Order chromosome names in proper genome order |
| cn | Get or Set the cn assayData slot |
| cn-method | Get or Set the cn assayData slot |
| cn2lr | Take vector or matrix of copynumber values, convert to log2ratios Utility function for converting copynumber units (2 is normal) to log2ratio units (two is normal) |
| cn<- | Get or Set the cn assayData slot |
| cn<--method | Get or Set the cn assayData slot |
| CNSet | Create a CNSet object |
| CNSet-class | Class '"CNSet"' |
| CNSet-defunct | Create a CNSet object |
| colMeans | Means of columns |
| colMeans-method | Means of columns |
| colnames | Get colnames from a GenoSet |
| colnames-method | Get colnames from a GenoSet |
| dim | Get start of location for each feature |
| dim-method | Get start of location for each feature |
| elementLengths | Get start of location for each feature |
| elementLengths-method | Get start of location for each feature |
| end | Get start of location for each feature |
| end-method | Get start of location for each feature |
| fake.baf | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| fake.cn | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| fake.lrr | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| fake.pData | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| featureNames | Get rownames from RangedData, GRanges, or GenoSet |
| featureNames-method | Get rownames from RangedData, GRanges, or GenoSet |
| featureNames<- | Get rownames from RangedData, GRanges, or GenoSet |
| featureNames<--method | Get rownames from RangedData, GRanges, or GenoSet |
| fixSegNAs | Fix NA runs in a Rle |
| gcCorrect | Correct copy number for GC content |
| genome | Get and set the genome universe annotation. |
| genome-method | Get and set the genome universe annotation. |
| genome<--method | Get and set the genome universe annotation. |
| genomeAxis | Label axis with base pair units |
| genoPlot | Plot data along the genome |
| genoPlot-method | Plot data along the genome |
| genoPlot-methods | Plot data along the genome |
| genoPos | Convert chromosome positions to positions from start of genome |
| genoPos-method | Convert chromosome positions to positions from start of genome |
| GenoSet | Create a GenoSet object |
| genoset | GenoSet: An eSet for data with genome locations |
| GenoSet-class | Class '"GenoSet"' |
| genoset-datasets | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| genoset-defunct | Defunct genoset features |
| genoset-deprecated | Deprecated genoset features |
| genoset.ds | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| initGenoSet | Create a GenoSet or derivative object |
| isGenomeOrder | Check if a GRanges, GenoSet or RangedData is in genome order |
| isGenomeOrder-method | Check if a GRanges, GenoSet or RangedData is in genome order |
| locData | Access the feature genome position info |
| locData-method | Access the feature genome position info |
| locData-methods | Access the feature genome position info |
| locData.gr | Example GenoSet, BAFSet, and CNSet objects and the data to create them. |
| locData<- | Access the feature genome position info |
| locData<--method | Access the feature genome position info |
| locData<--methods | Access the feature genome position info |
| lr2cn | Take vector or matrix of log2 ratios, convert to copynumber Utility function for converting log2ratio units (zero is normal) to copynumber units (two is normal) |
| lrr | Get lrr data |
| lrr-method | Get lrr data |
| lrr<- | Get lrr data |
| lrr<--method | Get lrr data |
| modeCenter | Center continuous data on mode |
| names | Get start of location for each feature |
| names-method | Get start of location for each feature |
| nrow | Get start of location for each feature |
| nrow-method | Get start of location for each feature |
| pos | Positions for features |
| pos-method | Positions for features |
| rangeColMeans | Calculate column means for multiple ranges |
| rangeSampleMeans | Average features in ranges per sample |
| rangeSegMeanLength | Get segment widths |
| rangeSegMeanLength-method | Get segment widths |
| readGenoSet | Load a GenoSet from a RData file |
| rownames | Get rownames from RangedData, GRanges, or GenoSet |
| rownames-method | Get rownames from RangedData, GRanges, or GenoSet |
| rownames<- | Get rownames from RangedData, GRanges, or GenoSet |
| rownames<--method | Get rownames from RangedData, GRanges, or GenoSet |
| runCBS | Run CBS Segmentation |
| sampleNames | Get colnames from a GenoSet |
| sampleNames-method | Get colnames from a GenoSet |
| sampleNames<- | Get colnames from a GenoSet |
| segPairTable | Convert Rle objects to tables of segments |
| segPairTable-method | Convert Rle objects to tables of segments |
| segs2Granges | GRanges from segment table |
| segs2RangedData | Make a RangedData from segments |
| segs2Rle | Make Rle from segments for one sample |
| segs2RleDataFrame | CBS segments to probe matrix |
| segTable | Convert Rle objects to tables of segments |
| segTable-method | Convert Rle objects to tables of segments |
| show | Show a GenoSet |
| show-method | Show a GenoSet |
| start | Get start of location for each feature |
| start-method | Get start of location for each feature |
| subsetAssayData | Subset assayData |
| toGenomeOrder | Set a GRanges, GenoSet, or RangedData to genome order |
| toGenomeOrder-method | Set a GRanges, GenoSet, or RangedData to genome order |
| universe-method | Get and set the genome universe annotation. |
| universe<--method | Get and set the genome universe annotation. |
| width | Get start of location for each feature |
| [ | Get start of location for each feature |
| [-method | Get start of location for each feature |
| [<- | Get start of location for each feature |
| [<--method | Get start of location for each feature |